Non‐perennial streams play a crucial role in ecological communities and the hydrological cycle. However, the key parameters and processes involved in stream intermittency remain poorly understood. While climatic conditions, geology and land use are well identified, the assessment and modelling of groundwater controls on streamflow intermittence remain a challenge. In this study, we explore new opportunities to calibrate process‐based 3D groundwater flow models designed to simulate hydrographic network dynamics in groundwater‐fed headwaters. Streamflow measurements and stream network maps are considered together to constrain the effective hydraulic properties of the aquifer in hydrogeological models. The simulations were then validated using visual observations of water presence/absence, provided by a national monitoring network in France (ONDE). We tested the methodology on two pilot unconfined shallow crystalline aquifer catchments, the Canut and Nançon catchments (Brittany, France). We found that both streamflow and stream network expansion/contraction dynamics are required to calibrate models that simultaneously estimate hydraulic conductivity and porosity with low uncertainties. The calibration allowed good prediction of stream intermittency, both in terms of flow and spatial extent. For the two catchments studied, Canut and Nançon, the hydraulic conductivity is close reaching 1.5 × 10−5 m/s and 4.5 × 10−5 m/s, respectively. However, they differ more in their storage capacity, with porosity estimated at 0.1% and 2.2%, respectively. Lower storage capacity leads to higher groundwater level fluctuations, shorter aquifer response times, an increase in the proportion of intermittent streams and a reduction in perennial flow. This new modelling framework for predicting headwater streamflow intermittence can be deployed to improve our understanding of groundwater controls in different geomorphological, geological and climatic contexts. It will benefit from advances in remote sensing and crowdsourcing approaches that generate new observational data products with high spatial and temporal resolution.